K. Adams and J. Palmer, Evolution of mitochondrial gene content: gene loss and transfer to the nucleus, Molecular Phylogenetics and Evolution, vol.29, issue.3, pp.380-395, 2003.
DOI : 10.1016/S1055-7903(03)00194-5

R. Al-reedy, R. Malireddy, C. Dillman, and J. Kennell, Comparative analysis of Fusarium mitochondrial genomes reveals a highly variable region that encodes an exceptionally large open reading frame, Fungal Genetics and Biology, vol.49, issue.1, pp.2-14, 2012.
DOI : 10.1016/j.fgb.2011.11.008

S. Amlacher, Insight into Structure and Assembly of the Nuclear Pore Complex by Utilizing the Genome of a Eukaryotic Thermophile, Cell, vol.146, issue.2, pp.277-289, 2011.
DOI : 10.1016/j.cell.2011.06.039

C. Barr, M. Neiman, and D. Taylor, Inheritance and recombination of mitochondrial genomes in plants, fungi and animals, New Phytologist, vol.359, issue.1, pp.39-50, 2005.
DOI : 10.1111/j.1469-8137.2005.01492.x

T. Bartelli, R. Ferreira, A. Colombo, and M. Briones, Intraspecific comparative genomics of Candida albicans mitochondria reveals non-coding regions under neutral evolution, Infection, Genetics and Evolution, vol.14, pp.302-312, 2013.
DOI : 10.1016/j.meegid.2012.12.012

L. Belcour, O. Begel, and M. Picard, A site-specific deletion in mitochondrial DNA of Podospora is under the control of nuclear genes., Proceedings of the National Academy of Sciences, vol.88, issue.9, pp.3579-3583, 1991.
DOI : 10.1073/pnas.88.9.3579

U. Bergthorsson, A. Richardson, G. Young, L. Goertzen, and J. Palmer, Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella, Proceedings of the National Academy of Sciences, vol.101, issue.51, pp.17747-17752, 2004.
DOI : 10.1073/pnas.0408336102

M. Bernt and M. Middendorf, A method for computing an inventory of metazoan mitochondrial gene order rearrangements, BMC Bioinformatics, vol.12, issue.Suppl 9, p.6, 2011.
DOI : 10.1093/bioinformatics/bti535

X. Bi and L. Liu, DNA rearrangement mediated by inverted repeats., Proceedings of the National Academy of Sciences, vol.93, issue.2, pp.819-823, 1996.
DOI : 10.1073/pnas.93.2.819

J. Boore, Animal mitochondrial genomes, Nucleic Acids Research, vol.27, issue.8, pp.1767-1780, 1999.
DOI : 10.1093/nar/27.8.1767

J. Boore and W. Brown, Complete DNA-sequence of the mitochondrial genome of the black chiton, Katharina tunicata, Genetics, vol.138, pp.423-443, 1994.

C. Bouchier, L. Ma, S. Creno, B. Dujon, and C. Fairhead, species reveal invasion by palindromic GC clusters and considerable size expansion, FEMS Yeast Research, vol.9, issue.8, pp.1283-1292, 2009.
DOI : 10.1111/j.1567-1364.2009.00551.x

T. Bruen, H. Philippe, and D. Bryant, A Simple and Robust Statistical Test for Detecting the Presence of Recombination, Genetics, vol.172, issue.4, pp.2665-2681, 2006.
DOI : 10.1534/genetics.105.048975

C. Bullerwell, G. Burger, and B. Lang, A novel motif for identifying Rps3 homologs in fungal mitochondrial genomes, Trends in Biochemical Sciences, vol.25, issue.8, pp.363-365, 2000.
DOI : 10.1016/S0968-0004(00)01612-1

C. Bullerwell and M. Gray, Evolution of the mitochondrial genome: protist connections to animals, fungi and plants, Current Opinion in Microbiology, vol.7, issue.5, pp.528-534, 2004.
DOI : 10.1016/j.mib.2004.08.008

C. Bullerwell and B. Lang, Fungal evolution: the case of the vanishing mitochondrion, Current Opinion in Microbiology, vol.8, issue.4, pp.362-369, 2005.
DOI : 10.1016/j.mib.2005.06.009

C. Bullerwell, J. Leigh, L. Forget, and B. Lang, A comparison of three fission yeast mitochondrial genomes, Nucleic Acids Research, vol.31, issue.2, pp.759-768, 2003.
DOI : 10.1093/nar/gkg134

G. Burger, M. Gray, and B. Lang, Mitochondrial genomes: anything goes, Trends in Genetics, vol.19, issue.12, pp.709-716, 2003.
DOI : 10.1016/j.tig.2003.10.012

S. Capella-gutierrez, J. Silla-martinez, and T. Gabaldon, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, vol.25, issue.15, pp.1972-1973, 2009.
DOI : 10.1093/bioinformatics/btp348

M. Cardoso, J. Tambor, and F. Nobrega, The mitochondrial genome from the thermal dimorphic fungusParacoccidioides brasiliensis, Yeast, vol.555, issue.7, pp.607-616, 2007.
DOI : 10.1002/yea.1500

R. Cedergren and B. Lang, Probing fungal mitochondrial evolution with tRNA, Biosystems, vol.18, issue.3-4, pp.263-267, 1985.
DOI : 10.1016/0303-2647(85)90026-7

A. Darling, B. Mau, and N. Perna, progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement, PLoS ONE, vol.15, issue.6, p.11147, 2010.
DOI : 10.1371/journal.pone.0011147.s005

J. Davila, Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis, BMC Biology, vol.9, issue.1, p.64, 2011.
DOI : 10.1186/1471-2105-7-439

S. Devine and J. Boeke, Integration of the yeast retrotransposon Ty1 is targeted to regions upstream of genes transcribed by RNA polymerase III., Genes & Development, vol.10, issue.5, pp.620-633, 1996.
DOI : 10.1101/gad.10.5.620

D. Rienzi, S. Collingwood, D. Raghuraman, M. Brewer, and B. , Fragile Genomic Sites Are Associated with Origins of Replication, Genome Biology and Evolution, vol.1, issue.0, pp.350-363, 2009.
DOI : 10.1093/gbe/evp034

I. Ebersberger, A Consistent Phylogenetic Backbone for the Fungi, Molecular Biology and Evolution, vol.29, issue.5, pp.1319-1334, 2012.
DOI : 10.1093/molbev/msr285

M. Eldarov, A. Mardanov, A. Beletsky, N. Ravin, and K. Skryabin, Complete sequence and analysis of the mitochondrial genome of the methylotrophic yeast Hansenula polymorpha DL-1, FEMS Yeast Research, vol.11, issue.6, pp.464-472, 2011.
DOI : 10.1111/j.1567-1364.2011.00736.x

C. Ferandon, The Agaricus bisporus cox1 Gene: The Longest Mitochondrial Gene and the Largest Reservoir of Mitochondrial Group I Introns, PLoS ONE, vol.5, issue.11, p.14048, 2010.
DOI : 10.1371/journal.pone.0014048.s003

G. Fischer, E. Rocha, F. Brunet, M. Vergassola, and B. Dujon, Highly variable rates of genome rearrangements between Hemiascomycetous yeast lineages, PLoS Genetics, vol.preprint, issue.2006, pp.253-261, 2006.
DOI : 10.1371/journal.pgen.0020032.eor

L. Forget, J. Ustinova, Z. Wang, V. Huss, and B. Lang, Hyaloraphidium curvatum: A Linear Mitochondrial Genome, tRNA Editing, and an Evolutionary Link to Lower Fungi, Molecular Biology and Evolution, vol.19, issue.3, pp.310-319, 2002.
DOI : 10.1093/oxfordjournals.molbev.a004084

E. Formighieri, The mitochondrial genome of the phytopathogenic basidiomycete Moniliophthora perniciosa is 109kb in size and contains a stable integrated plasmid, Mycological Research, vol.112, issue.10, pp.1136-1152, 2008.
DOI : 10.1016/j.mycres.2008.04.014

T. Gabaldon and M. Huynen, Reconstruction of the Proto-Mitochondrial Metabolism, Science, vol.301, issue.5633, pp.609-609, 2003.
DOI : 10.1126/science.1085463

T. Gabaldon and M. Huynen, Shaping the mitochondrial proteome, Biochimica et Biophysica Acta (BBA) - Bioenergetics, vol.1659, issue.2-3, pp.212-220, 2004.
DOI : 10.1016/j.bbabio.2004.07.011

T. Gabaldon and M. Huynen, From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism, PLoS Comput Biol, vol.3, pp.2209-2218, 2007.

T. Gabaldon, D. Rainey, and M. Huynen, Tracing the Evolution of a Large Protein Complex in the Eukaryotes, NADH:Ubiquinone Oxidoreductase (Complex I), Journal of Molecular Biology, vol.348, issue.4, pp.857-870, 2005.
DOI : 10.1016/j.jmb.2005.02.067

N. Galtier, The intriguing evolutionary dynamics of plant mitochondrial DNA, BMC Biology, vol.9, issue.1, p.61, 2011.
DOI : 10.1186/1471-2148-7-135

D. Ghikas, V. Kouvelis, and M. Typas, The complete mitochondrial genome of the entomopathogenic fungus Metarhizium anisopliae var. anisopliae: gene order and trn gene clusters reveal a common evolutionary course for all Sordariomycetes, while intergenic regions show variation, Archives of Microbiology, vol.13, issue.5, pp.393-401, 2006.
DOI : 10.1007/s00203-006-0104-x

D. Ghikas, V. Kouvelis, and M. Typas, Phylogenetic and biogeographic implications inferred by mitochondrial intergenic region analyses and ITS1-5.8S-ITS2 of the entomopathogenic fungi Beauveria bassiana and B. brongniartii, BMC Microbiology, vol.10, issue.1, p.174, 2010.
DOI : 10.1186/1471-2180-10-174

D. Gordenin, Inverted DNA repeats: a source of eukaryotic genomic instability., Molecular and Cellular Biology, vol.13, issue.9, pp.5315-5322, 1993.
DOI : 10.1128/MCB.13.9.5315

M. Gray, Genome structure and gene content in protist mitochondrial DNAs, Nucleic Acids Research, vol.26, issue.4, pp.865-878, 1998.
DOI : 10.1093/nar/26.4.865

S. Guindon, J. Dufayard, W. Hordijk, V. Lefort, and O. Gascuel, PhyML: fast and accurate phylogeny reconstruction by maximum likelihood, Infect Genet Evol, vol.9, pp.384-385, 2009.

J. Hane, Dothideomycete Plant Interactions Illuminated by Genome Sequencing and EST Analysis of the Wheat Pathogen Stagonospora nodorum, THE PLANT CELL ONLINE, vol.19, issue.11, pp.3347-3368, 2007.
DOI : 10.1105/tpc.107.052829

S. Haridas and J. Gantt, The mitochondrial genome of the wood-degrading basidiomycete Trametes cingulata, FEMS Microbiology Letters, vol.308, issue.1, pp.29-34, 2010.
DOI : 10.1111/j.1574-6968.2010.01979.x

J. Hecht, F. Grewe, and V. Knoop, Extreme RNA Editing in Coding Islands and Abundant Microsatellites in Repeat Sequences of Selaginella moellendorffii Mitochondria: The Root of Frequent Plant mtDNA Recombination in Early Tracheophytes, Genome Biology and Evolution, vol.3, issue.0, pp.344-358, 2011.
DOI : 10.1093/gbe/evr027

R. Hilker, C. Sickinger, C. Pedersen, and J. Stoye, UniMoG--a unifying framework for genomic distance calculation and sorting based on DCJ, Bioinformatics, vol.28, issue.19, pp.2509-2511, 2012.
DOI : 10.1093/bioinformatics/bts440

J. Huerta-cepas, J. Dopazo, and T. Gabaldon, ETE: a python Environment for Tree Exploration, BMC Bioinformatics, vol.11, issue.1, p.24, 2010.
DOI : 10.1186/1471-2105-11-24

A. Hughes and R. Friedman, Transposable Element Distribution in the Yeast Genome Reflects A Role in Repeated Genomic Rearrangement Events on an Evolutionary Time Scale, Genetica, vol.121, issue.2, pp.181-185, 2004.
DOI : 10.1023/B:GENE.0000040383.51611.e3

P. Jung, Complete mitochondrial genome sequence of the yeast Pichia farinosa and comparative analysis of closely related species, Current Genetics, vol.54, issue.6, pp.507-515, 2010.
DOI : 10.1007/s00294-010-0318-y

K. Kitazaki and T. Kubo, Cost of Having the Largest Mitochondrial Genome: Evolutionary Mechanism of Plant Mitochondrial Genome, Journal of Botany, vol.5, issue.4, 2010.
DOI : 10.1006/abbi.1998.0671

R. Kolpakov, G. Bana, and G. Kucherov, mreps: efficient and flexible detection of tandem repeats in DNA, Nucleic Acids Research, vol.31, issue.13, pp.3672-3678, 2003.
DOI : 10.1093/nar/gkg617
URL : https://hal.archives-ouvertes.fr/inria-00099597

V. Kouvelis, D. Ghikas, and M. Typas, The analysis of the complete mitochondrial genome of Lecanicillium muscarium (synonym Verticillium lecanii) suggests a minimum common gene organization in mtDNAs of Sordariomycetes: phylogenetic implications, Fungal Genetics and Biology, vol.41, issue.10, pp.930-940, 2004.
DOI : 10.1016/j.fgb.2004.07.003

A. Kueberl, High-quality genome sequence of Pichia pastoris CBS7435, Journal of Biotechnology, vol.154, issue.4, pp.312-320, 2011.
DOI : 10.1016/j.jbiotec.2011.04.014

A. Kurabayashi and R. Ueshima, Complete Sequence of the Mitochondrial DNA of the Primitive Opisthobranch Gastropod Pupa strigosa: Systematic Implication of the Genome Organization, Molecular Biology and Evolution, vol.17, issue.2, pp.266-277, 2000.
DOI : 10.1093/oxfordjournals.molbev.a026306

A. Lambowitz and P. Perlman, Involvement of aminoacyl-tRNA synthetases and other proteins in group I and group II intron splicing, Trends in Biochemical Sciences, vol.15, issue.11, pp.440-444, 1990.
DOI : 10.1016/0968-0004(90)90283-H

B. Lang, M. Laforest, and G. Burger, Mitochondrial introns: a critical view, Trends in Genetics, vol.23, issue.3, pp.119-125, 2007.
DOI : 10.1016/j.tig.2007.01.006

D. Lavrov, Rapid Proliferation of Repetitive Palindromic Elements in mtDNA of the Endemic Baikalian Sponge Lubomirskia baicalensis, Molecular Biology and Evolution, vol.27, issue.4, pp.757-760, 2010.
DOI : 10.1093/molbev/msp317

D. Lavrov, J. Boore, and W. Brown, Complete mtDNA Sequences of Two Millipedes Suggest a New Model for Mitochondrial Gene Rearrangements: Duplication and Nonrandom Loss, Molecular Biology and Evolution, vol.19, issue.2, pp.163-169, 2002.
DOI : 10.1093/oxfordjournals.molbev.a004068

J. Lazowska, C. Jacq, and P. Slonimski, Sequence of introns and flanking exons in wild-type and box3 mutants of cytochrome b reveals an interlaced splicing protein coded by an intron, Cell, vol.22, issue.2, pp.333-348, 1980.
DOI : 10.1016/0092-8674(80)90344-X

C. Levings and G. Brown, Molecular biology of plant mitochondria, Cell, vol.56, issue.2, pp.171-179, 1989.
DOI : 10.1016/0092-8674(89)90890-8

J. Litter, A. Keszthelyi, Z. Hamari, I. Pfeiffer, and J. Kucsera, Differences in Mitochondrial Genome Organization of Cryptococcus Neoformans Strains, Antonie van Leeuwenhoek, vol.9, issue.Suppl. 2, pp.249-255, 2005.
DOI : 10.1007/s10482-005-8544-x

Y. Liu, J. Xue, B. Wang, L. Li, and Y. Qiu, The Mitochondrial Genomes of the Early Land Plants Treubia lacunosa and Anomodon rugelii: Dynamic and Conservative Evolution, PLoS ONE, vol.6, issue.10, p.25836, 2011.
DOI : 10.1371/journal.pone.0025836.s002

K. Lobachev, Factors affecting inverted repeat stimulation of recombination and deletion in Saccharomyces cerevisiae, Genetics, vol.148, pp.1507-1524, 1998.

R. Lucking, S. Huhndorf, D. Pfister, E. Plata, and H. Lumbsch, Fungi evolved right on track, Mycologia, vol.101, issue.6, pp.810-822, 2009.
DOI : 10.3852/09-016

M. Lynch and J. Blanchard, Deleterious mutation accumulation in organelle genomes, Genetica, pp.102-10329, 1998.
DOI : 10.1007/978-94-011-5210-5_3

M. Lynch, B. Koskella, and S. Schaack, Mutation Pressure and the Evolution of Organelle Genomic Architecture, Science, vol.311, issue.5768, pp.1727-1730, 2006.
DOI : 10.1126/science.1118884

M. Marcet-houben and T. Gabaldon, The Tree versus the Forest: The Fungal Tree of Life and the Topological Diversity within the Yeast Phylome, PLoS ONE, vol.301, issue.2, p.4357, 2009.
DOI : 10.1371/journal.pone.0004357.s010

D. Martin, P. Lemey, and D. Posada, Analysing recombination in nucleotide sequences, Molecular Ecology Resources, vol.38, issue.Suppl. 1, pp.943-955, 2011.
DOI : 10.1111/j.1755-0998.2011.03026.x

D. Martin, RDP3: a flexible and fast computer program for analyzing recombination, Bioinformatics, vol.26, issue.19, pp.2462-2463, 2010.
DOI : 10.1093/bioinformatics/btq467

J. Maydt and T. Lengauer, Recco: recombination analysis using cost optimization, Bioinformatics, vol.22, issue.9, pp.1064-1071, 2006.
DOI : 10.1093/bioinformatics/btl057

B. Nabholz, S. Glemin, and N. Galtier, The erratic mitochondrial clock: variations of mutation rate, not population size, affect mtDNA diversity across birds and mammals, BMC Evolutionary Biology, vol.9, issue.1, p.54, 2009.
DOI : 10.1186/1471-2148-9-54

M. Neiman and D. Taylor, The causes of mutation accumulation in mitochondrial genomes, Proceedings of the Royal Society B: Biological Sciences, vol.272, issue.1578, pp.1201-1209, 2009.
DOI : 10.1093/molbev/msg167

C. Notredame, D. Higgins, and J. Heringa, T-coffee: a novel method for fast and accurate multiple sequence alignment, Journal of Molecular Biology, vol.302, issue.1, pp.205-217, 2000.
DOI : 10.1006/jmbi.2000.4042

M. Odahara, H. Kuroiwa, T. Kuroiwa, and Y. Sekine, Suppression of Repeat-Mediated Gross Mitochondrial Genome Rearrangements by RecA in the Moss Physcomitrella patens, THE PLANT CELL ONLINE, vol.21, issue.4, pp.1182-1194, 2009.
DOI : 10.1105/tpc.108.064709

J. Palmer, Dynamic evolution of plant mitochondrial genomes: Mobile genes and introns and highly variable mutation rates, Proceedings of the National Academy of Sciences, vol.97, issue.13, pp.6960-6966, 2000.
DOI : 10.1073/pnas.97.13.6960

M. Pantou, V. Kouvelis, and M. Typas, The complete mitochondrial genome of Fusarium oxysporum: Insights into fungal mitochondrial evolution, Gene, vol.419, issue.1-2, pp.7-15, 2008.
DOI : 10.1016/j.gene.2008.04.009

B. Paquin and B. Lang, The Mitochondrial DNA of Allomyces macrogynus: The Complete Genomic Sequence from an Ancestral Fungus, Journal of Molecular Biology, vol.255, issue.5, pp.688-701, 1996.
DOI : 10.1006/jmbi.1996.0056

B. Paquin, The fungal mitochondrial genome project: evolution of fungal mitochondrial genomes and their gene expression, Current Genetics, vol.31, issue.5, pp.380-395, 1997.
DOI : 10.1007/s002940050220

S. Pellenz, A. Harington, B. Dujon, K. Wolf, and B. Schafer, Characterization of the I-Spom I Endonuclease from Fission Yeast: Insights into the Evolution of a Group I Intron-Encoded Homing Endonuclease, Journal of Molecular Evolution, vol.55, issue.3, pp.302-313, 2002.
DOI : 10.1007/s00239-001-2327-4

M. Perseke, Evolution of mitochondrial gene orders in echinoderms, Molecular Phylogenetics and Evolution, vol.47, issue.2, pp.855-864, 2008.
DOI : 10.1016/j.ympev.2007.11.034

N. Phadnis, R. Sia, and E. Sia, Analysis of Repeat-Mediated Deletions in the Mitochondrial Genome of Saccharomyces cerevisiae, Genetics, vol.171, issue.4, pp.1549-1559, 2005.
DOI : 10.1534/genetics.105.047092

D. Posada and K. Crandall, Evaluation of methods for detecting recombination from DNA sequences: Computer simulations, Proceedings of the National Academy of Sciences, vol.98, issue.24, pp.13757-13762, 2001.
DOI : 10.1073/pnas.241370698

E. Prochazka, S. Polakova, J. Piskur, and P. Sulo, Mitochondrial genome from the facultative anaerobe and petite-positive yeast Dekkera bruxellensis???contains the NADH dehydrogenase subunit genes, FEMS Yeast Research, vol.10, pp.545-557, 2010.
DOI : 10.1111/j.1567-1364.2010.00644.x

R. Development and C. , R: a language and environment for statistical computing [Internet]. Vienna (Austria): R Foundation for Statistical Computing, 2011.

T. Rawlings, T. Collins, and R. Bieler, A Major Mitochondrial Gene Rearrangement Among Closely Related Species, Molecular Biology and Evolution, vol.18, issue.8, pp.1604-1609, 2001.
DOI : 10.1093/oxfordjournals.molbev.a003949

E. Rocha, DNA repeats lead to the accelerated loss of gene order in bacteria, Trends in Genetics, vol.19, issue.11, pp.600-603, 2003.
DOI : 10.1016/j.tig.2003.09.011

E. Rocha, Inference and Analysis of the Relative Stability of Bacterial Chromosomes, Molecular Biology and Evolution, vol.23, issue.3, pp.513-522, 2006.
DOI : 10.1093/molbev/msj052

E. Rocha, A. Danchin, and A. Viari, Functional and evolutionary roles of long repeats in prokaryotes, Research in Microbiology, vol.150, issue.9-10, pp.725-733, 1999.
DOI : 10.1016/S0923-2508(99)00120-5

A. Rokas, E. Ladoukakis, and E. Zouros, Animal mitochondrial DNA recombination revisited, Trends in Ecology & Evolution, vol.18, issue.8, pp.411-417, 2003.
DOI : 10.1016/S0169-5347(03)00125-3

C. Saccone, Mitochondrial DNA in metazoa: degree of freedom in a frozen event, Gene, vol.286, issue.1, pp.3-12, 2002.
DOI : 10.1016/S0378-1119(01)00807-1

C. Sacerdot, Promiscuous DNA in the nuclear genomes of hemiascomycetous yeasts, FEMS Yeast Research, vol.8, issue.6, pp.846-857, 2008.
DOI : 10.1111/j.1567-1364.2008.00409.x
URL : https://hal.archives-ouvertes.fr/hal-00315493

M. Sanderson, r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock, Bioinformatics, vol.19, issue.2, pp.301-302, 2003.
DOI : 10.1093/bioinformatics/19.2.301

E. Seif, L. Forget, N. Martin, and B. Lang, Mitochondrial RNase P RNAs in ascomycete fungi: Lineage-specific variations in RNA secondary structure, RNA, vol.9, issue.9, pp.1073-1083, 2003.
DOI : 10.1261/rna.5880403

E. Seif, Comparative mitochondrial genomics in zygomycetes: bacteria-like RNase P RNAs, mobile elements and a close source of the group I intron invasion in angiosperms, Nucleic Acids Research, vol.33, issue.2, pp.734-744, 2005.
DOI : 10.1093/nar/gki199

D. Sloan, Rapid Evolution of Enormous, Multichromosomal Genomes in Flowering Plant Mitochondria with Exceptionally High Mutation Rates, PLoS Biology, vol.39, issue.1, p.1001241, 2012.
DOI : 10.1371/journal.pbio.1001241.s011

C. Specht, C. Novotny, and R. Ullrich, Mitochondrial DNA of Schizophyllum commune: restriction map, genetic map, and mode of inheritance, Current Genetics, vol.12, issue.2, pp.129-134, 1992.
DOI : 10.1007/BF00351472

A. Stamatakis, RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models, Bioinformatics, vol.22, issue.21, pp.2688-2690, 2006.
DOI : 10.1093/bioinformatics/btl446

J. Tamames, Evolution of gene order conservation in prokaryotes, 2001.

J. Taylor and M. Berbee, Dating divergences in the Fungal Tree of Life: review and new analyses, Mycologia, vol.98, issue.6, pp.838-849, 2006.
DOI : 10.1080/15572536.2006.11832614

G. Tesler, GRIMM: genome rearrangements web server, Bioinformatics, vol.18, issue.3, pp.492-493, 2002.
DOI : 10.1093/bioinformatics/18.3.492

S. Torriani, S. Goodwin, G. Kema, J. Pangilinan, and B. Mcdonald, Intraspecific comparison and annotation of two complete mitochondrial genome sequences from the plant pathogenic fungus Mycosphaerella graminicola, Fungal Genetics and Biology, vol.45, issue.5, pp.628-637, 2008.
DOI : 10.1016/j.fgb.2007.12.005

T. Tuller, Association between translation efficiency and horizontal gene transfer within microbial communities, Nucleic Acids Research, vol.39, issue.11, pp.4743-4755, 2011.
DOI : 10.1093/nar/gkr054

A. Van-diepeningen, Mitochondrial recombination increases with age in Podospora anserina, Mechanisms of Ageing and Development, vol.131, issue.5, pp.315-322, 2010.
DOI : 10.1016/j.mad.2010.03.001

J. Vaughn, M. Mason, G. Sperwhitis, P. Kuhlman, and J. Palmer, Fungal origin by horizontal transfer of a plant mitochondrial group I intron in the chimeric coxI gene of Peperomia, Journal of Molecular Evolution, vol.41, issue.5, pp.563-572, 1995.
DOI : 10.1007/BF00175814

C. Vlcek, W. Marande, S. Teijeiro, J. Lukes, and G. Burger, Systematically fragmented genes in a multipartite mitochondrial genome, Nucleic Acids Research, vol.39, issue.3, pp.979-988, 2011.
DOI : 10.1093/nar/gkq883

A. Waldman, H. Tran, E. Goldsmith, and M. Resnick, Long inverted repeats are an at-risk motif for recombination in mammalian cells, Genetics, vol.153, pp.1873-1883, 1999.

Y. Wang, F. Zeng, C. Hon, Y. Zhang, and F. Leung, (oyster mushroom), FEMS Microbiology Letters, vol.280, issue.1, pp.34-41, 2008.
DOI : 10.1111/j.1574-6968.2007.01048.x

K. Wolfe, W. Li, and P. Sharp, Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs., Proceedings of the National Academy of Sciences, vol.84, issue.24, pp.9054-9058, 1987.
DOI : 10.1073/pnas.84.24.9054

K. Wolfe and D. Shields, Molecular evidence for an ancient duplication of the entire yeast genome, Nature, vol.387, issue.6634, pp.708-713, 1997.
DOI : 10.1038/42711

P. Woo, is more closely related to those of molds than yeasts, FEBS Letters, vol.41, issue.3, pp.469-477, 2003.
DOI : 10.1016/S0014-5793(03)01307-3

Y. Wu, Recent dermatophyte divergence revealed by comparative and phylogenetic analysis of mitochondrial genomes, BMC Genomics, vol.10, issue.1, p.238, 2009.
DOI : 10.1186/1471-2164-10-238

B. Xavier, V. Miao, Z. Jonsson, and O. Andresson, Mitochondrial genomes from the lichenized fungi Peltigera membranacea and Peltigera malacea: Features and phylogeny, Fungal Biology, vol.116, issue.7, pp.802-814, 2012.
DOI : 10.1016/j.funbio.2012.04.013

N. Yamazaki, Evolution of pulmonate gastropod mitochondrial genomes: comparisons of gene organizations of Euhadra, Cepaea and Albinaria and implications of unusual tRNA secondary structures, Genetics, vol.145, pp.749-758, 1997.

Y. Zivanovic, P. Wincker, B. Vacherie, M. Bolotin-fukuhara, and H. Fukuhara, Complete nucleotide sequence of the mitochondrial DNA from, FEMS Yeast Research, vol.5, issue.4-5, pp.315-322, 2005.
DOI : 10.1016/j.femsyr.2004.09.003
URL : https://hal.archives-ouvertes.fr/hal-00198575